ISEP - DM – Engenharia Biomédica
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Percorrer ISEP - DM – Engenharia Biomédica por autor "Adão, Diogo José de Oliveira"
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- Development of a flexible graphical interface for the Pegi3s Phenotypic Evolution GroupPublication . Adão, Diogo José de Oliveira; Coelho, Luís Filipe Martins PintoSequence data, representing full genomes, exomes, or transcriptomes, is increasingly important in biomedical research and practice. However, the ongoing shortfall of bioinformaticians since the 1990s poses a major challenge. Consequently, easy-to-use bioinformatics applications tailored for researchers without an informatics background are essential. In the software context, Linux container technologies, particularly Docker, offer a solution due to their many advantages. Docker images provide ready-to-use software packages with all necessary dependencies installed, making deployment easy on any operating system with Docker. This eliminates the often difficult and sometimes impossible task of installing software dependencies. Docker images are immutable, enhancing reproducibility, and facilitate the development of complex pipelines, standalone applications with GUIs, and databases. These features help address the reproducibility crisis in bioinformatics analyses. Pegi3s (Phenotypic Evolution Group) is responsible for maintaining the Bioinformatics Docker Images Project, a growing collection with over 100 Docker images of software typically used in the fields of genomics, transcriptomics, proteomics, phylogenetics, sequence manipulation, among others During the development of this project, a new virtual machine was developed with a newer version of Ubuntu relative to the previously used virtual machine. Due to some software updates, it became necessary the development of a software that allowed the user to manage his images (Docker Manager). All images from the pegi3s were reviewed and a standardized set of Test Data was created for most of them. With this Test Data, it was obtained the results for the execution of most programs. With the obtained information, “DocNRun pegi3s” was created, a software that allows the user to run Docker images without using the Command Line. Currently, both Docker Manager and DocNRun exist in the pegi3s repositories available for anyone to pull.